The Mixed Lineage Leukemia (MLL) gene located on chromosome 11q23 is a frequent site of translocation that results in a number of oncogenic fusion proteins. MLL-translocations are present in a variety of paediatric and adult leukaemias and are associated with poor survival outcome. Despite intense research efforts the mechanisms underlying the leukaemogenic activity of MLL-translocations are poorly understood. Our aim was to identify proteins involved in leukaemogenesis that are regulated by MLL-translocation gene expression through quantitative proteome analysis using a leukaemia model. Our model of acute myeloid leukaemia (AML) is controlled by the regulated expression of a common MLL-translocation gene, MLL-AF9. Initially, surface captured proteins were analysed over a time course using a SILAC quantitative proteomics workflow and high-resolution mass spectrometry to generate a profile of proteins that are expressed in the presence or absence of MLL-AF9 expression. We extended this analysis by also profiling changes to the entire leukaemia proteome during MLL-AF9 regulation. The results from these two techniques have not only confirmed several known targets in AML but highlighted novel pathways and targets that are upregulated when MLL-AF9 is expressed. These pathways include epigenetic regulators, cell signalling and cell-cell or cell-extracellular matrix interactions. The results from this study not only identify mechanisms by which MLL-AF9 regulates leukaemogenesis, but also demonstrate the potential identification of biomarkers and novel drug targets.